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The HotKnots program predicts secondary structures of RNA molecules with or without pseudoknots. The HotKnots algorithm has been described by Ren et al [2]. New parameters have been estimated by Andronescu et al [1]. The source code of HotKnots, together with data and results obtained in [1], can be obtained from here.



[1] Andronescu, M., Pop, C., and Condon, A., Improved energy parameters for RNA pseudoknotted secondary structure prediction, RNA. 2010 Jan;16(1):26-42.

[2] Ren, J., Rastegari, B., Condon, A., and Hoos, H. H. (2005). HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11(10), 1494--1504.